Deck 10 - Shuttlebays 1 and 2, with NPC contact to allow selection of small craft.

Deck 11 - Main Engineering with Engineering Officer DOff contact (I'd personally move the Ops Officer DOff contact to the bridge, possibly having the later automatically use the costume of whoever's my Chief of Ops)

Talaxian Bridge Officers and Playable Species to be released at the same time for same price as Ferasan for Federation accounts.
Kazon Bridge Officers and Playable Species to be released at the same time for same price as Ferasan for KDF accounts.

But only when an FE for the Delta Quadrant has been opened up.

Now, for some of my own suggestions:

Perhaps an unlockable Captain's Yacht variant - the never-seen Voyager Aeroshuttle? - Basically, 400-Day Veterans who have the Captain's Yacht AND have bought the Voyager bundle would get an alternative skin for their flyable Yacht.

Allow the user to toggle the LCARS color scheme - the canon multicolored ones or the 2400 blue theme.

Each room should be modular, so that in the future if Cryptic uses Neverwinter's Foundry system to allow players to customise ship interiors room by room, said players would be able to expand on the ship interiors themselves.